Zheng Tracy Ke

Jiashun Jin, Zheng Tracy Ke, Paxton Turner et al.

How to detect a small community in a large network is an interesting problem, including clique detection as a special case, where a naive degree-based $χ^2$-test was shown to be powerful in the presence of an Erdős-Renyi background. Using Sinkhorn's theorem, we show that the signal captured by the $χ^2$-test may be a modeling artifact, and it may disappear once we replace the Erdős-Renyi model by a broader network model. We show that the recent SgnQ test is more appropriate for such a setting. The test is optimal in detecting communities with sizes comparable to the whole network, but has never been studied for our setting, which is substantially different and more challenging. Using a degree-corrected block model (DCBM), we establish phase transitions of this testing problem concerning the size of the small community and the edge densities in small and large communities. When the size of the small community is larger than $\sqrt{n}$, the SgnQ test is optimal for it attains the computational lower bound (CLB), the information lower bound for methods allowing polynomial computation time. When the size of the small community is smaller than $\sqrt{n}$, we establish the parameter regime where the SgnQ test has full power and make some conjectures of the CLB. We also study the classical information lower bound (LB) and show that there is always a gap between the CLB and LB in our range of interest.

Dieyi Chen, Jiashun Jin, Zheng Tracy Ke

Subject clustering (i.e., the use of measured features to cluster subjects, such as patients or cells, into multiple groups) is a problem of great interest. In recent years, many approaches were proposed, among which unsupervised deep learning (UDL) has received a great deal of attention. Two interesting questions are (a) how to combine the strengths of UDL and other approaches, and (b) how these approaches compare to one other. We combine Variational Auto-Encoder (VAE), a popular UDL approach, with the recent idea of Influential Feature PCA (IF-PCA), and propose IF-VAE as a new method for subject clustering. We study IF-VAE and compare it with several other methods (including IF-PCA, VAE, Seurat, and SC3) on $10$ gene microarray data sets and $8$ single-cell RNA-seq data sets. We find that IF-VAE significantly improves over VAE, but still underperforms IF-PCA. We also find that IF-PCA is quite competitive, which slightly outperforms Seurat and SC3 over the $8$ single-cell data sets. IF-PCA is conceptually simple and permits delicate analysis. We demonstrate that IF-PCA is capable of achieving the phase transition in a Rare/Weak model. Comparatively, Seurat and SC3 are more complex and theoretically difficult to analyze (for these reasons, their optimality remains unclear).

Tianchen Gao, Jiashun Jin, Zheng Tracy Ke et al.

Recently, DeepSeek has been the focus of attention in and beyond the AI community. An interesting problem is how DeepSeek compares to other large language models (LLMs). There are many tasks an LLM can do, and in this paper, we use the task of predicting an outcome using a short text for comparison. We consider two settings, an authorship classification setting and a citation classification setting. In the first one, the goal is to determine whether a short text is written by human or AI. In the second one, the goal is to classify a citation to one of four types using the textual content. For each experiment, we compare DeepSeek with $4$ popular LLMs: Claude, Gemini, GPT, and Llama. We find that, in terms of classification accuracy, DeepSeek outperforms Gemini, GPT, and Llama in most cases, but underperforms Claude. We also find that DeepSeek is comparably slower than others but with a low cost to use, while Claude is much more expensive than all the others. Finally, we find that in terms of similarity, the output of DeepSeek is most similar to those of Gemini and Claude (and among all $5$ LLMs, Claude and Gemini have the most similar outputs). In this paper, we also present a fully-labeled dataset collected by ourselves, and propose a recipe where we can use the LLMs and a recent data set, MADStat, to generate new data sets. The datasets in our paper can be used as benchmarks for future study on LLMs.

Jiashun Jin, Zheng Tracy Ke, Gabriel Moryoussef et al.

Given a $K$-vertex simplex in a $d$-dimensional space, suppose we measure $n$ points on the simplex with noise (hence, some of the observed points fall outside the simplex). Vertex hunting is the problem of estimating the $K$ vertices of the simplex. A popular vertex hunting algorithm is successive projection algorithm (SPA). However, SPA is observed to perform unsatisfactorily under strong noise or outliers. We propose pseudo-point SPA (pp-SPA). It uses a projection step and a denoise step to generate pseudo-points and feed them into SPA for vertex hunting. We derive error bounds for pp-SPA, leveraging on extreme value theory of (possibly) high-dimensional random vectors. The results suggest that pp-SPA has faster rates and better numerical performances than SPA. Our analysis includes an improved non-asymptotic bound for the original SPA, which is of independent interest.

Yicong Jiang, Zheng Tracy Ke

Vertex hunting (VH) is the task of estimating a simplex from noisy data points and has many applications in areas such as network and text analysis. We introduce a new variant, semi-supervised vertex hunting (SSVH), in which partial information is available in the form of barycentric coordinates for some data points, known only up to an unknown transformation. To address this problem, we develop a method that leverages properties of orthogonal projection matrices, drawing on novel insights from linear algebra. We establish theoretical error bounds for our method and demonstrate that it achieves a faster convergence rate than existing unsupervised VH algorithms. Finally, we apply SSVH to two practical settings, semi-supervised network mixed membership estimation and semi-supervised topic modeling, resulting in efficient and scalable algorithms.

Morgane Austern, Yuanchuan Guo, Zheng Tracy Ke et al.

Topic modeling is traditionally applied to word counts without accounting for the context in which words appear. Recent advancements in large language models (LLMs) offer contextualized word embeddings, which capture deeper meaning and relationships between words. We aim to leverage such embeddings to improve topic modeling. We use a pre-trained LLM to convert each document into a sequence of word embeddings. This sequence is then modeled as a Poisson point process, with its intensity measure expressed as a convex combination of $K$ base measures, each corresponding to a topic. To estimate these topics, we propose a flexible algorithm that integrates traditional topic modeling methods, enhanced by net-rounding applied before and kernel smoothing applied after. One advantage of this framework is that it treats the LLM as a black box, requiring no fine-tuning of its parameters. Another advantage is its ability to seamlessly integrate any traditional topic modeling approach as a plug-in module, without the need for modifications Assuming each topic is a $β$-Hölder smooth intensity measure on the embedded space, we establish the rate of convergence of our method. We also provide a minimax lower bound and show that the rate of our method matches with the lower bound when $β\leq 1$. Additionally, we apply our method to several datasets, providing evidence that it offers an advantage over traditional topic modeling approaches.

Zhirui Hu, Zheng Tracy Ke, Jun S Liu

The success of deep learning has inspired recent interests in applying neural networks in statistical inference. In this paper, we investigate the use of deep neural networks for nonparametric regression with measurement errors. We propose an efficient neural network design for estimating measurement error models, in which we use a fully connected feed-forward neural network (FNN) to approximate the regression function $f(x)$, a normalizing flow to approximate the prior distribution of $X$, and an inference network to approximate the posterior distribution of $X$. Our method utilizes recent advances in variational inference for deep neural networks, such as the importance weight autoencoder, doubly reparametrized gradient estimator, and non-linear independent components estimation. We conduct an extensive numerical study to compare the neural network approach with classical nonparametric methods and observe that the neural network approach is more flexible in accommodating different classes of regression functions and performs superior or comparable to the best available method in nearly all settings.

Jiashun Jin, Zheng Tracy Ke, Shengming Luo

A network may have weak signals and severe degree heterogeneity, and may be very sparse in one occurrence but very dense in another. SCORE (Jin, 2015) is a recent approach to network community detection. It accommodates severe degree heterogeneity and is adaptive to different levels of sparsity, but its performance for networks with weak signals is unclear. In this paper, we show that in a broad class of network settings where we allow for weak signals, severe degree heterogeneity, and a wide range of network sparsity, SCORE achieves prefect clustering and has the so-called "exponential rate" in Hamming clustering errors. The proof uses the most recent advancement on entry-wise bounds for the leading eigenvectors of the network adjacency matrix. The theoretical analysis assures us that SCORE continues to work well in the weak signal settings, but it does not rule out the possibility that SCORE may be further improved to have better performance in real applications, especially for networks with weak signals. As a second contribution of the paper, we propose SCORE+ as an improved version of SCORE. We investigate SCORE+ with 8 network data sets and found that it outperforms several representative approaches. In particular, for the 6 data sets with relatively strong signals, SCORE+ has similar performance as that of SCORE, but for the 2 data sets (Simmons, Caltech) with possibly weak signals, SCORE+ has much lower error rates. SCORE+ proposes several changes to SCORE. We carefully explain the rationale underlying each of these changes, using a mixture of theoretical and numerical study.

Yaqi Duan, Zheng Tracy Ke, Mengdi Wang

State aggregation is a popular model reduction method rooted in optimal control. It reduces the complexity of engineering systems by mapping the system's states into a small number of meta-states. The choice of aggregation map often depends on the data analysts' knowledge and is largely ad hoc. In this paper, we propose a tractable algorithm that estimates the probabilistic aggregation map from the system's trajectory. We adopt a soft-aggregation model, where each meta-state has a signature raw state, called an anchor state. This model includes several common state aggregation models as special cases. Our proposed method is a simple two-step algorithm: The first step is spectral decomposition of empirical transition matrix, and the second step conducts a linear transformation of singular vectors to find their approximate convex hull. It outputs the aggregation distributions and disaggregation distributions for each meta-state in explicit forms, which are not obtainable by classical spectral methods. On the theoretical side, we prove sharp error bounds for estimating the aggregation and disaggregation distributions and for identifying anchor states. The analysis relies on a new entry-wise deviation bound for singular vectors of the empirical transition matrix of a Markov process, which is of independent interest and cannot be deduced from existing literature. The application of our method to Manhattan traffic data successfully generates a data-driven state aggregation map with nice interpretations.

Zheng Tracy Ke

In the probabilistic topic models, the quantity of interest---a low-rank matrix consisting of topic vectors---is hidden in the text corpus matrix, masked by noise, and the Singular Value Decomposition (SVD) is a potentially useful tool for learning such a low-rank matrix. However, the connection between this low-rank matrix and the singular vectors of the text corpus matrix are usually complicated and hard to spell out, so how to use SVD for learning topic models faces challenges. In this paper, we overcome the challenge by revealing a surprising insight: there is a low-dimensional simplex structure which can be viewed as a bridge between the low-rank matrix of interest and the SVD of the text corpus matrix, and allows us to conveniently reconstruct the former using the latter. Such an insight motivates a new SVD approach to learning topic models, which we analyze with delicate random matrix theory and derive the rate of convergence. We support our methods and theory numerically, using both simulated data and real data.

Jiashun Jin, Zheng Tracy Ke, Wanjie Wang

Consider a two-class clustering problem where we observe $X_i = \ell_i μ+ Z_i$, $Z_i \stackrel{iid}{\sim} N(0, I_p)$, $1 \leq i \leq n$. The feature vector $μ\in R^p$ is unknown but is presumably sparse. The class labels $\ell_i\in\{-1, 1\}$ are also unknown and the main interest is to estimate them. We are interested in the statistical limits. In the two-dimensional phase space calibrating the rarity and strengths of useful features, we find the precise demarcation for the Region of Impossibility and Region of Possibility. In the former, useful features are too rare/weak for successful clustering. In the latter, useful features are strong enough to allow successful clustering. The results are extended to the case of colored noise using Le Cam's idea on comparison of experiments. We also extend the study on statistical limits for clustering to that for signal recovery and that for hypothesis testing. We compare the statistical limits for three problems and expose some interesting insight. We propose classical PCA and Important Features PCA (IF-PCA) for clustering. For a threshold $t > 0$, IF-PCA clusters by applying classical PCA to all columns of $X$ with an $L^2$-norm larger than $t$. We also propose two aggregation methods. For any parameter in the Region of Possibility, some of these methods yield successful clustering. We find an interesting phase transition for IF-PCA. Our results require delicate analysis, especially on post-selection Random Matrix Theory and on lower bound arguments.